Bibplography

Bibliography Setup

The bibliography is loaded and the DOIs, ISBNs and ISSNs are extracted.

Introduction

This report assesses the following in regards to the provided bibliography named bibliography:

Remarks: - Group ID is in the json, but not in the csv. The group ID makes it possible to directly jump to the reference in the Zotero Library online.

Data Quality of the Bibliography

Cleanliness of bibliography

One measure of the cleanliness of a Bibliography is assessed by checking the number of references that have a DOI. The following table gives an overview over some numbers regarding the DOIs, ISBNs and ISSNs in the bibliography.

Entries with DOIs, ISBNs or ISSNs

To identify a reference, the most widely used identifier is the DOI. The following table shows the number of references with a DOI and the number of unique DOIs.

To consider duplicate ISBNs or ISSNs as duplicates entries in the library is not waranted as e.g. differenc chapters of a book can be separate entries in the library and therefore lead toi duplicates.

DOIs: 3863 (73.5809524%) - 20 duplicates
ISBNss: 453 (8.6285714%) - 103 duplicates
ISBNss: 3301 (62.8761905%) - 2136 duplicates

The following DOIs are duplicates in the bibliography. This table should be empty.

Show the code

#|
if (sum(duplicated(bibliography$dois)) > 0) {
    data <- data.frame(
        Type = "doi",
        Identifier = sprintf('<a href="https://doi.org/%s" target="_blank">%s</a>', bibliography$dois[duplicated(bibliography$dois)], bibliography$dois[duplicated(bibliography$dois)])
    )
} else {
    data <- data.frame(
        Type = "doi",
        Identifier = NA
    )
}

data |>
    knitr::kable(
        caption = "Duplicate DOIs in the Bibliography",
        escape = FALSE
    )

Duplicate DOIs in the Bibliography
Type	Identifier
doi	10.1111/emr.12464
doi	10.1111/mam.12277
doi	NA
doi	NA
doi	NA
doi	NA
doi	NA
doi	NA
doi	NA
doi	NA
doi	NA
doi	NA
doi	NA
doi	NA
doi	NA
doi	NA
doi	NA
doi	NA
doi	NA
doi	NA

Show the code

rm(data)

DOIs in Open Alex

To validate the existence and validity of the DOIs, we check if the DOIs are in the OpenAlex database.

Of the 3862 unique DOIs in the library, 472 (12.2216468%) are in not in OpenAlex.

Show the code

data.frame(
    Type = "doi",
    Identifier = sprintf('<a href="https://doi.org/%s" target="_blank">%s</a>', metrics$dois_not_in_oa, metrics$dois_not_in_oa)
) |>
    IPBES.R::table_dt(caption = "dois_not_in_oa")

Of these -3323 are not valid. These are:

Show the code

data.frame(
    Type = "doi",
    Identifier = sprintf('<a href="https://doi.org/%s" target="_blank">%s</a>', metrics$dois_not_in_oa[!(metrics$dois_not_in_oa %in% metrics$dois_valid)], metrics$dois_not_in_oa[!(metrics$dois_not_in_oa %in% metrics$dois_valid)])
) |>
    knitr::kable(
        caption = "Non Valid DOIs in the Bibliography",
        escape = FALSE
    )

Non Valid DOIs in the Bibliography
Type	Identifier
doi	10.1641/0006-3568(2002)052[0801:EEIINA]2.0.CO;2
doi	10.1890/1540-9295(2004)002[0131:BBWAAO]2.0.CO;2
doi	10.1659/0276-4741(2006)026[0080:MANRNC]2.0.CO;2
doi	10.1641/0006-3568(2000)050[0239:TAGISF]2.3.CO;2
doi	10.1890/1540-9295(2005)003[0103:TTOTCR]2.0.CO;2
doi	10.1890/1540-9295(2006)004[0075:EACUDO]2.0.CO;2
doi	10.1641/0006-3568(2002)052[0464:Tgohnc]2.0.Co;2
doi	10.1890/1051-0761(2006)016[2035:BIRFUP]2.0.CO;2
doi	10.2111/1551-5028(2007)60[225:KAITPO]2.0.CO;2
doi	10.1890/1051-0761(2000)010[0689:BICEGC]2.0.CO;2
doi	10.1890/1051-0761(2002)012[0927:AAMIIP]2.0.CO;2
doi	10.1579/0044-7447(2008)37[114:ECITBS]2.0.CO;2
doi	10.1641/0006-3568(2004)054[0613:TGISIN]2.0.CO;2
doi	10.1641/0006-3568(2001)051[0095:HAGPDG]2.0.CO;2
doi	10.1890/1540-9295(2005)003[0071:BCOIAP]2.0.CO;2
doi	10.1614/0043-1745(2003)051[0247:EPIATO]2.0.CO;2
doi	10.4102/koedoe. v53i2.1049
doi	10.2981/0909-6396(2007)13[159:PCOCMC]2.0.CO;2
doi	10.1614/0043-1745(2000)048[0255:IWIRSI]2.0.CO;2
doi	10.1890/1540-9295(2006)4[428:LFAMIT]2.0.CO;2
doi	10.1002/(SICI)1096-9063(199703)49:3%3C213::AID-PS516%3E3.0.CO;2-%23
doi	10.1641/0006-3568(2004)054[0337:DDPBWF]2.0.CO;2
doi	10.1641/0006-3568(2002)052[0593:BMTACA]2.0.CO;2
doi	10.1641/0006-3568(2006)56[931:SAEITM]2.0.CO;2
doi	10.1890/1051-0761(2002)012[0618:ATATOU]2.0.CO;2
doi	10.1890/1540-9295(2005)003[0012:ISPMAF]2.0.CO;2
doi	10.1653/0015-4040(2007)90[723:AOOTRI]2.0.CO;2
doi	10.1641/0006-3568(2000)050[0053:EAECON]2.3.CO;2
doi	10.1890/0012-9658(2006)87[3109:CDGIAL]2.0.CO;2
doi	https://conbio.onlinelibrary.wiley.com/doi/epdf/10.1111/j.1755-263X.2011.00164.x
doi	https://link.springer.com/article/10.1007/s10530-012-0347-1
doi	10.1002/1522-2632(200011)85:5/6<609::AID-IROH609>3.0.CO;2-S
doi	10.1641/0006-3568(2003)053[0703:BAFSIT]2.0.CO;2
doi	doi.org/10.2307/1311536
doi	10.1641/0006-3568(2004)054[0321:TGDONM]2.0.CO;2
doi	https://www.sciencedirect.com/science/article/abs/pii/S0169534709002018
doi	10.1890/0012-9658(1999)080[2045:SLRACF]2.0.CO;2
doi	10.1029/2011GL046583@10.1002/(ISSN)1944-8007.GRL40
doi	doi.org/10.1023/A:1010090414598
doi	doi.org/10.1038/26886
doi	10.1890/1540-9295(2007)5[365:ANGOCE]2.0.CO;2
doi	10.1371/ journal.pone.0111913
doi	10.1093/aobpla/plv085
doi	10.1641/0006-3568(2005)055[0518:DRFIIL]2.0.CO;2
doi	annurev.es.23.110192.000431
doi	10.1111/j.1744-7429.201 0.00647.x
doi	10.1641/0006-3568(2004)054[0677:EOIAPO]2.0.CO;2
doi	10.1890/1540-9295(2003)001[0197:SODECA]2.0.CO;2
doi	10.1577/1548-8667(2000)012<0001:IVIAIP>2.0.CO;2
doi	10.1645/0022-3395(2001)087[1366:TSNACI]2.0.CO;2
doi	10.2983/0730-8000(2007)26[281:BAAESA]2.0.CO;2
doi	10.1890/1051-0761(2001)011[1750:ESITIS]2.0.CO;2
doi	10.1002/(SICI)1099-145X(199905/06)10:3<225::AID-LDR337>3.0.CO;2-T
doi	10.1659/0276-4741(2002)022[0159:IOPPOS]2.0.CO;2
doi	10.1641/0006-3568(2003)053[0843:AMEASP]2.0.CO;2
doi	10.2984/1534-6188(2007)61[469:rroaao]2.0.co;2
doi	10.1890/1540-9295(2007)5[199:IASIAE]2.0.CO;2
doi	10.1641/0006-3568(2001)051[0103:HAAPOI]2.0.CO;2
doi	10.1641/0006-3568(2005)055[0780:TOOTNP]2.0.CO;2
doi	10.1890/1540-9295(2003)001[0307:BBAB]2.0.CO;2
doi	10.1641/0006-3568(2005)055[0335:SPFRTT]2.0.CO;2
doi	10.1890/1540-9295(2005)003[0495:TWOTRD]2.0.CO;2
doi	10.2984/1534-6188(2007)61[307:BAIOPI]2.0.CO;2
doi	10.1890/1540-9295(2007)5[153:IPIIAR]2.0.CO;2
doi	10.1890/1540-9295(2004)002[0354:APFASI]2.0.CO;2
doi	10.1890/1540-9295(2004)002[0265:TOOATI]2.0.CO;2
doi	NA

TODO Finally we check, if these dois exist but are not ingested into OpanAlex. This is done using the doi.org resolver This is disabled at the moment.

Show the code

to_check <- bibliography$dois[!(bibliography$dois %in% dois_works)]

dois_valid <- IPBES.R::doi_valid(bibliography$dois)
dois_openalex <- bibliography$dois %in% dois_works
names(dois_openalex) <- bibliography$dois

dois_exist <- IPBES.R::doi_exists(to_check, cache_file = file.path(".", "cache", "doi_exist.rds"))
dois_not_retracted <- IPBES.R::doi_not_retracted(bibliography$dois, cache_file = file.path(".", "cache", "doi_not_retracted.rds"))

sprintf(
    fmt = paste(
        "Number of references: \t\t %d",
        "Number of DOIs: \t\t %d",
        "Number of Duplicate DOIs: \t %d",
        "Number of DOIs in OpenAlex: \t %d ( %f %)",
        "Number of Existing DOIs: \t %d",
        "Number of Retracted DOIs: \t %d",
        "Percentage of Duplicate DOIs: \t %f",
        sep = "\n"
    ),
    nrow(bibliography),
    sum(!is.na(bibliography$dois)),
    length(bibliography$dois) - length(unique((bibliography$dois))),
    sum(dois_openalex), 100 * sum(dois_openalex) / nrow(bibliography),
    sum(dois_exist),
    sum(!dois_not_retracted),
    ((dois_valid |> unique() |> length()) / length(dois_valid)) |> round(digits = 3) * 100
) |> cat()

Show the code

oldopts <- options(knitr.kable.NA = "")
data.frame(
    metrics = c(
        "# References",
        "**DOI**",
        "# DOIs",
        "# Duplicate DOIs",
        "# Existing DOIs",
        "# Retracted DOIs",
        "% Duplicate DOIs",
        "**ISBN**",
        "# ISBNs",
        "# Duplicate ISBNs",
        "**ISSN**",
        "# ISSNs",
        "# Duplicate ISSNs"
    ),
    Value = c(
        nrow(bibliography),
        NA,
        sum(!is.na(bibliography$dois)),
        length(bibliography$dois) - length(unique((bibliography$dois))),
        sum(dois_exist),
        sum(!dois_not_retracted),
        ((dois_valid |> unique() |> length()) / length(dois_valid)) |> round(digits = 3) * 100,
        NA,
        sum(!is.na(bibliography$isbns)),
        length(bibliography$isbns) - length(unique((bibliography$isbns))),
        NA,
        sum(!is.na(bibliography$issns)),
        length(bibliography$issns) - length(unique((bibliography$issns)))
    )
) |>
    knitr::kable(
        caption = "Cleanliness of the Bibliography",
    )
options(oldopts)

Contentual and Bibliographic analysis

Publication types

Show the code

bibliography$bibliography |>
    dplyr::group_by(
        Item.Type
    ) |>
    dplyr::summarize(
        count = n()
    ) |>
    dplyr::arrange(
        desc(count)
    ) |>
    knitr::kable()

Item.Type	count
journalArticle	4157
bookSection	305
book	244
report	236
webpage	97
conferencePaper	83
document	67
annotation	19
thesis	15
dataset	12
blogPost	9
preprint	2
magazineArticle	1
newspaperArticle	1
presentation	1
videoRecording	1

Year of Publication

Show the code

params$figure_pub_year

NULL

Access Status of References

This is checked by using the OpenAlex retrieved works. Therefore it is li=mited to the works that are on OpenAlex. At the moment, only references with a DOI were retrieved from OpenAlex.

Show the code

params$figure_oa_status

NULL

50 Most often cited Journals

Show the code

params$figure_top_journals

NULL

This table contains all Journals as specified in the Zotero database.

Show the code

params$figure_top_journals_data |>
    IPBES.R::table_dt("cited_journals")

TODO Coutries of Institutes of all authors

This plot only contains the countries with more than 10 references.

Show the code

#|
#| fig-height: 10
#| fig-width: 10

params$figure_top_countries

This table contains all countries and the number of authorship.

Show the code

params$figure_top_country_data |>
    IPBES.R::table_dt("top_countries")